Overview

• Total strains : 773
• Total SNVs before filter : 4,118,149
• Total SNVs after filter : 2,633,263
• Total indels before filter : 1,435,679
• Total indels after filter : 563,912

Site-level quality filters

Number of variant sites removed by each filter

Each bar shows counts of variant sites removed by the combinations of filters indicated by the dots below.

Pre-filter statistics

Variant counts for each strain based on vcf containing all variant sites called by GATK (“soft-filter.vcf”).

Post-filter statistics

Variant count for each strain based on the VCF containing only sites pass all filters (“hard-filter.vcf”). All heterozygous sites on main chromosomes were converted to either homozygous or missing. The remaining heterozygous sites are all located on mitochondria chromosomes.